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Clinical Chemistry 53: 1577-1584, 2007. First published July 18, 2007; 10.1373/clinchem.2007.087361
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(Clinical Chemistry. 2007;53:1577-1584.)
© 2007 American Association for Clinical Chemistry, Inc.

Molecular Diagnostics and Genetics

A Simple and Robust Quantitative PCR Assay to Determine CYP21A2 Gene Dose in the Diagnosis of 21-Hydroxylase Deficiency

Silvia Parajes1, Celsa Quinterio1, Fernando Domínguez1,2 and Lourdes Loidi1,a

1 Fundación Pública Gallega de Medicina Genómica (Unidad de Medicina Molecular), Santiago de Compostela, Spain.
2 Universidad de Santiago de Compostela, Departamento de Fisiología, Santiago de Compostela, Spain.

aAddress correspondence to this author at: Unidad de Medicina Molecular, Fundación Pública Gallega de Medicina Genómica, Hospital Clínico Universitario, 15706 Santiago de Compostela, Spain. Fax 34-981951473; e-mail lloidi{at}usc.es.


   Abstract
Top
 Abstract
Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Background: Correct diagnosis of 21-hydroxylase deficiency (21OHD) requires the identification of CYP21A2 gene deletions and CYP21A1P/CYP21A2 chimeric genes, which are disease-causing alleles, and gene duplications, which can lead to false-positive 21OHD allele results. Because lack of suitable CYP21A2 dosage assessment methods hampers correct 21OHD diagnosis, we developed a new assay based on the relative quantification of the CYP21A2 gene using the DSP gene as a reference.

Methods: The assay to determine CYP21A2 copy number is based on real-time PCR. The method also detects the presence of the CYP21A1P/CYP21A2 chimeric gene. We used a duplex PCR to coamplify the DSP gene, included as an internal control, along with CYP21A2. The difference in threshold cycles between CYP21A2 and DSP genes ({Delta}Ct) was used to assess CYP21A2 copy number.

Results: The {Delta}Ct values obtained from 24 samples used to set up the method clearly differentiated 3 nonoverlapping intervals, which corresponded to the number of CYP21A2 copies: –1.35 to –0.25 defined 2 gene copies, +0.20 to +2.00 defined 1 copy, and –2.50 to –1.50 defined 3 copies. With these intervals we were able to assess the gene copy number in 24 additional samples.

Conclusions: This new method for gene copy assessment detects homozygous and heterozygous CYP21A2 gene deletions, CYP21A1P/CYP21A2 chimeric genes, and gene duplications. Moreover, the method is robust, fast, and easy to use in a molecular diagnosis laboratory. This method together with CYP21A2 gene sequencing can provide a definitive system for the detection of almost all, common as well as rare, 21OHD alleles.


   Introduction
Top
 Abstract
 Introduction
Materials and Methods
 Results
 Discussion
 References
 
Congenital adrenal hyperplasia is an autosomal recessive disorder caused in 90%–95% of cases by a 21-hydroxylase deficiency (21OHD) 1 (OMIM +201910), which leads to impaired synthesis of cortisol. 21OHD shows highly variable phenotypical expression, and cases are commonly classified as either classical or nonclassical forms. The absence of steroid 21-hydroxylase (21OH; EC 1.14.99.10) activity results in the classical form of 21OHD, which manifests as a salt-wasting form, in which neither cortisol nor aldosterone can be synthesized, and by the simple virilizing form, in which residual activity of 21OH allows aldosterone synthesis. The nonclassical form occurs when partial 21OH activity is present. This form is late onset and may be asymptomatic or associated with signs of postnatal androgen excess (1).

The 21OH enzyme is encoded by the CYP21A2 2 (older nomenclature, CYP21, CYP21B) gene, which is 98% homologous to the CYP21A1P pseudogene (older nomenclature: CYP21P, CYP21A) in its coding sequence and 96% homologous in introns. Both genes lie in the human MHC at chromosome 6p21.3, a highly variable stretch of DNA. Most chromosomes bear 1 CYP21A1P pseudogene and 1 CYP21A2 gene, although deletions and duplications have been described (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Intergenic recombinations are relatively frequent in this region (14), and are responsible for 95% of the mutations associated with 21OHD; the remaining 5% of mutations are apparently not the result of gene conversion events (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). Among the intergenic recombinations, approximately 75% are deleterious or partially inactivating mutations, which are typically present in the CYP21A1P pseudogene and appear in the CYP21A2 gene as a result of gene conversion events (14). These mutations are easily detected by CYP21A2 gene sequencing, restriction digestion, or other methods (15). The remaining 20%–25% of mutations are CYP21A2 gene deletions or CYP21A1P/CYP21A2 chimeric genes formed by unequal meiotic crossover (1)(14)(15). Such mutations lead to the absence of 21OH activity and thus are very important for 21OHD diagnosis and carrier detection (2)(4)(5)(6)(10)(11)(13)(16). Other unequal meiotic crossover arrangements can produce duplicated CYP21A2 genes, which have been found in Dutch (12), Swedish (4)(8), Italian (6), and other populations, mainly with the presence of the severe Gln318X or I2G (c.293-13 A/C>G GenBank Ref. ID NM000500, according to the Human Genome Variation Society) mutations in 1 of the CYP21A2 genes (8)(12). Consequently, to avoid false-positive results, assessment of the CYP21A2 gene copy number is very important when a mutation is present, especially the Gln318X or I2G mutation.

Until now such large rearrangements have been mainly detected by Southern blot analysis (17)(18), which is time-consuming, highly laborious, and requires large amounts of DNA. To avoid such limitations, PCR-based amplification analyses have been developed (19)(20)(21)(22)(23)(24)(25), but some of these have failed in CYP21A2 duplication detection (21)(23)(24)(25).

We report a real-time quantitative PCR (qPCR)-based method for the easy and rapid detection of these large rearrangements. The method can detect CYP21A2 deletions, CYP21A1P/CYP21A2 chimeric genes, and also CYP21A2 duplications.


   Materials and Methods
Top
 Abstract
 Introduction
 Materials and Methods
Results
 Discussion
 References
 
dna samples
DNA samples from 24 persons were used for the development of the quantitative method. Seven of these individuals were carriers of 2 copies of the CYP21A2 gene, 5 were carriers of only 1 copy of the gene, 2 were carriers of the G110del8nt deleterious mutation (c.331_338del8 GenBank Ref. ID NM000500, according to the Human Genome Variation Society), 7 were carriers of 3 copies, 2 had no copies, and 1 was homozygous for the G110del8nt mutation. Once the method was developed and the criteria to assess gene copy numbers were established, we confirmed the method in an independent set of samples from 24 persons randomly selected from samples sent to our laboratory because 21OHD was suspected. In all cases, DNA was extracted from peripheral blood leukocytes by standard procedures. All study participants gave informed consent, and the procedures were approved by our institution’s ethics committee.

genotyping of the samples
Sequencing and Southern blot.
The CYP21A2 gene sequencing and the Southern blot for the 24 samples used to develop the assay were carried out as previously described (26) and enabled the assessment of the CYP21A2 copy number. Thus, the presence of 2 copies of the CYP21A2 gene was assumed for individuals who were compound heterozygous for mutations or polymorphisms in the gene.

Southern blot analysis revealed that 5 individuals had only 1 copy of the CYP21A2 gene, due to gene deletion or to CYP21A2/CYP21A1P chimeric gene formation. Direct PCR product sequencing revealed the presence of the G110del8nt mutation in 2 heterozygous individuals. These 2 samples were further grouped with the samples with 1 gene copy because the primer (P3S) used for the qPCR annealed to the wild-type gene at the 110-codon stretch. It is important to point out that the Southern blot pattern of these 2 samples would be normal and different from CYP21A2 gene deletions and CYP21A1P/CYP21A2 chimeric genes.

The absence of CYP21A2 gene copies due to homozygous gene deletion was assessed by Southern blot analysis in 2 individuals. The presence of a homozygous G110del8nt mutation was determined in 1 individual by gene sequencing. Like the samples described above, this sample would show a normal Southern blot pattern, but it was included in the group of no CYP21A2 copies.

Finally, the presence of 3 copies of the gene was determined by direct sequencing in 2 individuals: 1 individual was a carrier of the I2G, Ile172Asn, and Gln318X mutations and possessed 3 different alleles at the –13 position in intron 2 (SNP rs6467 A/C plus the G mutation); in the 2nd individual the presence of a 3rd copy of the gene was demonstrated by the presence of heterozygosis along the 1st PCR product, despite the presence of Ile236Asn, Val237Glu, and Met239Lys mutations, which prevented the antisense primer from binding on this allele. Results for both of these individuals were confirmed by Southern blot. A 3rd individual, identified from a prenatal diagnosis sample, had 3 copies of the CYP21A2 gene and was a compound heterozygous female with 2 severe mutations: Gln318X inherited from her mother and Gly291Ser inherited from her father. The duplication of the gene in 1 allele was suspected because of an unbalanced allele ratio in the sequencing electropherogram at the Gln318X mutation in the mother DNA as well as in the fetus. Gene duplication in 1 allele was later confirmed by the finding that 17-OH progesterone concentrations were within the reference interval in the amniotic fluid and by fetal echography showing ordinary female external genitalia. Four more individuals with 3 copies of the gene were characterized by gene sequencing. All of these individuals displayed the unbalanced Gln318X mutation in the electropherogram. This mutation was present in a particular haplotype, which was also present in the other 2 individuals with 3 copies; this haplotype presented 2 uncommon polymorphisms, a G>A change in intron 2 at position –79 and a C>T change at nucleotide 13 in the 3' UTR region of the gene.

gene dose assessment by real-time qPCR
PCR primers and probes.
For the quantification of the CYP21A2 gene copy number, we amplified a fragment of 132 bp in size that extended from exon 3 to intron 3. The forward primer used for this amplification was 5'-ACC TGT CCT TGG GAG ACT AC-3' (P3S), which allowed the specific amplification of the CYP21A2 gene, because it annealed to a segment of exon 3 when the G110del8nt mutation was not present. The reverse primer was 5'-TTA CCT CAC AGA ACT CCT GGG T-3' (BI3A). The MGB-TaqMan® probe (Applied Biosystems) used for the quantification was designed 7 bp away from the end of the P3S primer, and the sequence was 5'-TCT GGA AAG CCC ACA-3', with FAM dye at the 5' end as reporter.

The quantification has been assessed as relative to the DSP gene in a duplex qPCR. To obtain greater similarity among both PCRs, we followed the same criteria for the DSP primers and probe design as for the CYP21A2 gene. Accordingly, we amplified a fragment of 132 bp in size, extending along exon 2 of the DSP gene, by use of the forward primer 5'-TGC CTC CTT AGT CAA ACC GG-3' (DSP-S) and the reverse 5'-GGA ACA GGG AAA GCT TAC AGG-3' (DSP-A). The sequence of the MGB-TaqMan probe (Applied Biosystems) for the DSP gene was 5'-TCC AGG CAC CAG AA-3' with VIC dye as reporter.

duplex pcr conditions
The 2 fragments described above were simultaneously amplified in the same well in a 25-µL reaction containing 1x TaqMan Universal PCR Master Mix, No AmpErase® UNG (Applied Biosystems), 900 nmol/L of each CYP21A2 primer, 1080 nmol/L of each DSP primer, 250 nmol/L of each probe, and 50–200 ng of DNA. The reaction was subjected to 95 °C for 10 min, followed by 40 cycles of 95 °C for 15 s and 60 °C for 1 min in an ABI7300 Real-Time PCR System (Applied Biosystems). Data were analyzed with the 7300 System SDS Software (Version 1.3.1.21).

assessment of cyp21a2 and dsp pcr efficiency
The efficiencies of the CYP21A2 and DSP PCRs were assessed with the dilution series method (27), in which threshold cycle (Ct) values were plotted against the logarithm of the input amount of DNA. The duplex PCRs previously described were carried out in triplicate with 8 serial dilutions, from 1:1 to 1:500, starting with 250 ng of template DNA. Then we performed calibration curves by plotting the Ct values against the logarithms of input DNA. Slope values from –3.90 to –3.20 were considered adequate because they correlated with 80%–105% PCR efficiencies. The efficiency was calculated for templates with 3, 2, and 1 CYP21A2 copy.

assessment of cyp21a2 copy number
To assess the CYP21A2 copy number, the difference in Ct ({Delta}Ct) for CYP21A2 and DSP genes was calculated and plotted against the logarithm of the CYP21A2:DSP ratios (%) (ratio of CYP21A2 and DSP copy number). The resulting curves obtained through linear regression analysis were used to calculate the CYP21A2 copy number.

assessment of the method variability
The SD and the CV (%) of {Delta}Ct values and the CYP21A2:DSP ratios obtained were used to determine the variability of the method. For intraassay variation, the 24 samples used for the method development were run in duplicate in the same plate; and for the interassay variation, the plates were run on 3 different days.

The variation due to the amount of DNA used in the assay was assessed from {Delta}Cts and CYP21A2:DSP ratios obtained with 50 ng, 100 ng, and 200 ng of input DNA for the 3 groups of samples: 1, 2, and 3 gene copies.

statistical analyses
The linear regression, the ANOVA test, and data plots were performed with the SPSS version 12.0 for Windows and Instant version 3.33 programs.


   Results
Top
 Abstract
 Introduction
 Materials and Methods
 Results
Discussion
 References
 
cyp21a2 and dsp pcrs efficiency
The efficiency rates for the CYP21A2 gene PCR were 81%, 84%, and 99% for templates with 3, 2, and 1 gene copy, respectively, and for the DSP gene PCR were 84% for templates with 3 and 2 CYP21A2 gene copies and 95% for templates with 1 copy (Fig. 1 ). These results were obtained with dye fluorescence threshold values of 0.055 and 0.05 for CYP21A2 and DSP genes, respectively, and an automatic baseline. Regression linear analysis for {Delta}Ct values and the logarithm of the input amount of DNA showed slopes <0.1 for all the templates, indicating that the efficiencies for both genes were very similar.


Figure 1
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  		Figure 1. CYP21A2 and DSP calibration curves calculated from Ct data of 1:1 to 1:500 dilutions for templates with 3, 2, or 1 CYP21A2 copy.

Open diamonds represent Ct values for CYP21A2 gene and circles represent Ct values for DSP gene. Intercepts (B), slopes (S), correlation coefficients (r2) as well as their SD (SDB, SDS, and SDres, respectively), and efficiency (E) were calculated for each gene according to the CYP21A2 copy number. These data are noted below each graph.

{Delta}ct results
The mean (SD) {Delta}Ct obtained, taking into account the results of all the plates with 100 ng of input DNA, were –1.91 (0.20) for samples with 3 CYP21A2 gene copies, –0.86 (0.17) for samples with 2 copies, and +0.80 (0.29) for samples with 1 copy. Similar results were obtained with 50 ng and 200 ng of DNA (Table 1 ). The ANOVA tests showed no significant differences in {Delta}Ct values between samples with the same number of copies; these differences became significant, however, when we compared {Delta}Ct values for samples with a different number of copies (P <0.001) for 100 ng of template DNA, as well as for 50 ng and 200 ng (Fig. 2 ).


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  		Table 1. {Delta}Ct values and CYP21A2:DSP ratios obtained from data of plate replicates.1


Figure 2
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  		Figure 2. Scatterplot of {Delta}Ct values obtained with 100 ng of DNA corresponding to the 21 analyzed samples and their replicates, according to the CYP21A2 copy number studied.

Squares represent samples with 3 CYP21A2 copies; circles represent samples with 2 copies, and triangles represent samples with 1 CYP21A2 copy. The samples homozygous for the CYP21A2 deletion and G110del8nt mutation are not plotted.

assessment of cyp21a2 copy number
Based on the results of the duplex PCR described in Materials and Methods, we considered samples with amplification of the DSP gene but without amplification of the CYP21A2 gene to be deficient in functional CYP21A2 genes. This result was found in the 2 samples homozygous for the gene deletion and in the sample homozygous for the G110del8nt mutation. The samples with 1 or more CYP21A2 copies showed amplification for both genes, and we inferred the number of copies, as described in Materials and Methods (see Fig. 1Up in the Data Supplement that accompanies the online version of this article at http://www.clinchem.org/contents/vol53/issue9). The mean (SD) CYP21A2:DSP ratios, taking into account the results of all the plates with 100 ng of sample DNA, were 1.45 (0.11) for samples with 3 CYP21A2 copies, 1.05 (0.07) for samples with 2 copies, and 0.52 (0.06) for samples with 1 copy (Table 1Up ). The ANOVA test, which we applied to the slopes of the curves so that the reproducibility of the method could be assessed, revealed no significant differences. Similar results were obtained with 50 ng and 200 ng of sample DNA (Tables 1Up and 2 ).


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  		Table 2. Slopes from linear regression studies for plate replicates using 50, 100, and 200 ng of DNA.1

assay variation
Intraassay variation.
The {Delta}Ct variability values [mean (SD)] when the method was performed with 100 ng of DNA were 13% [–1.93 (0.25)], 20% [–0.77 (0.16)], and 47% [+0.79 (0.37)], corresponding to 3, 2, and 1 CYP21A2 copy, respectively. These results are similar to those observed for 50 ng of DNA and slightly lower than those observed for 200 ng (data not shown). The 99% CIs were –2.14 to –1.72, –0.90 to –0.64, and +0.48 to +1.10 for 3, 2, and 1 CYP21A2 copy, respectively; these CIs as well as the {Delta}Ct intervals obtained from mean and SD values did not overlap.

The intrassay variation for the CYP21A2:DSP ratios [mean (SD)] were 10% [1.51 (0.15)], 6% [0.97 (0.06)], and 15% [0.54 (0.08)] for samples with 3, 2, and 1 CYP21A2 copy, respectively. The reported data and the 99% CIs, (1.37–1.65), (0.92–1.02), and (0.48–0.60), for the 3 groups were clearly separated as they were when 50 ng and 200 ng of input DNA were used (data not shown).

Interassay variation.
The interassay variation obtained from {Delta}Ct values was 10% for samples with 3 CYP21A2 copies, 20% for carriers of 2 copies, and 36% for samples with 1 copy. The mean (SD) {Delta}Ct and the 99% CIs calculated for the different CYP21A2 copy numbers did not overlap. Similar results were found for 50 ng of DNA, and results were slightly higher when 200 ng of DNA was added to the reaction (Table 1Up ).

The interassay variation for the CYP21A2:DSP ratios was 8% for 3, 7% for 2, and 11% for 1 gene copy. Again, the mean (SD) ratios and the 99% CIs calculated in each case did not overlap, as was the case when 50 ng and 200 ng of input DNA were used (Table 1Up ).

Variation induced by the amount of DNA.
The variation induced in the {Delta}Ct values by the amount of DNA was 15% for samples with 3 gene copies, 21% for samples with 2 copies, and 39% for samples with 1 gene copy. The variability rates induced in the CYP21A2:DSP ratios were 9%, 7%, and 13% for samples with 3, 2, and 1 copy, respectively (Table 3 ).


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  		Table 3. Variability in CYP21A2 copy number related to the amount of DNA added to the reaction.

criterion for the cyp21a2 copy number assessment
The reported data allow the establishment of the criterion for the assessment of the CYP21A2 copy number. Thus, a sample is diagnosed as having 2 CYP21A2 copies when {Delta}Ct values are between –1.35 and –0.25. A heterozygous chimeric CYP21A1P/CYP21A2 gene or CYP21A2 deletion is determined by {Delta}Ct values between +0.20 and +2.00, and heterozygous duplication is diagnosed by {Delta}Ct values between –2.50 and –1.50. A homozygous chimeric CYP21A1P/CYP21A2 gene or CYP21A2 deletion is assigned by the absence of CYP21A2 gene amplification in the presence of DSP gene amplification. In any case, DSP Ct values have to be <27 for 100 ng and <29 for 50 ng of input DNA.

{Delta}ct values of the 24 additional samples
These 24 additional samples were analyzed in duplicate and showed the following {Delta}Ct values: –1.30 to –0.33 in 21 samples, –2.45 to –2.19 in 2 samples, and +0.77 to +0.85 in 1 sample.


   Discussion
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
References
 
Southern blot analysis has long been the reference method for the detection of large deletions and of CYP21A1P/CYP21A2 chimeric genes associated with 21OHD. Nevertheless, this method requires large quantities of DNA and is too laborious and time-consuming to be routinely used for 21OHD molecular diagnosis (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28).

To facilitate diagnosis of gross deletions and chimeric genes, other strategies have been developed. Most of these methods are based on PCR (19)(20)(21)(22)(23)(24) or real-time qPCR (25), but most fail to detect CYP21A2 gene duplications (21)(23)(25), a shortcoming that can lead to misidentification of a nonpathological allele with 2 CYP21A2 genes, 1 mutated plus 1 wild type, as a pathological 21OHD allele (12).

Taking into account all the problems and limitations of current methods for 21OHD diagnosis, we developed a new method based on the relative quantification of the CYP21A2 gene using the DSP gene as a reference. The DSP gene was chosen as the reference gene because it is located on chromosome 6, as is CYP21A2, and no variations in its copy number have been described in the Database of Genomic Variation (http://projects.tcag.ca/variation/). In both cases, primers and probes annealed to a region of the genome where no polymorphisms have been described to date. Any such variation in DSP primers and/or probe DNA sample binding sites that impaired amplification would produce an increase in Ct values of this gene, and the sample would not be considered for analysis; a possible CYP21A2 allele dropout due to the presence of variations under the PCR primers and/or probe would be detected by sequencing. On the other hand, the high specificity of the CYP21A2 qPCR was demonstrated by the absence of CYP21A1P amplification in samples with no CYP21A2 gene copies.

We validated the duplex PCR, confirming by serial dilution method that PCR efficiency was optimal (81%–99%) and similar for CYP21A2 and DSP genes for the 3 templates tested (27) (Fig. 1Up ). These results were also confirmed by the independence of {Delta}Ct values of the amount of DNA analyzed; nevertheless, variability was higher with 200 ng than with smaller amounts of sample DNA. Therefore, 50–100 ng of input DNA for the analysis is recommended. After method validation, we used linear regression studies to assess CYP21A2 copy number. The CYP21A2 copy number obtained for each sample tested, expressed as the ratio of the CYP21A2 and DSP gene copies, was in accord with the results obtained by Southern blot and direct sequencing.

Although we initially assessed CYP21A2 copy number through linear regression studies, we later found that estimations of {Delta}Ct values could be used to assess copy number, because the ranges of {Delta}Ct values were clearly separated into 3 groups according to the CYP21A2 gene copy number (Fig. 2Up ). Moreover, intra- and interassay variation analyses showed that these 3 defined groups did not overlap. Therefore, we used {Delta}Ct values directly for the CYP21A2 copy number assessment, avoiding the CYP21A2:DSP ratio calculation and thus facilitating the analysis. In all of the samples, the results obtained in this way were concordant with the results obtained by Southern blot combined with sequencing. The results of the 3 samples without CYP21A2 gene copies were also concordant with Southern blot and sequencing results. The {Delta}Ct values obtained with the 24 additional samples fulfilled the criterion previously established. Therefore we found that the samples could be ascribed to 1 of the 3 defined groups: 21 samples had 2 CYP21A2 gene copies, 2 samples had 3 copies, and 1 sample had a heterozygous gene deletion or chimeric gene. These samples were further analyzed by sequencing and Southern blot when necessary, and the results were concordant.

The main limitation of this method, with respect to the Southern blot, is lack of characterization of the arrangement of CYP21A1P and CYP21A2 genes; however, for 21OHD diagnostic purposes, carrier detection, genetic counseling, and prenatal diagnosis, it is essential to know the exact functional gene copy number that an individual has, whereas detailed knowledge of this arrangement is less important.

In summary, the present method offers an accurate alternative to Southern blot and other methods described previously for 21OHD diagnosis and has the following advantages: (a) it requires only a small amount of DNA (50–100 ng); (b) it is neither time-consuming (2 h) nor laborious, and can analyze many samples simultaneously; and (c) it is effective in the detection of CYP21A2 gene duplication, which is one of its most important advantages (21)(23)(25).

In conclusion, the proposed method is easy to use in a molecular diagnosis laboratory and together with the CYP21A2 gene sequencing might be a definitive way to detect almost all, common as well as rare, 21OHD alleles.


   Acknowledgments
 
Grant/funding support: L.L. has support from Fondo Invetigaciones Sanitarios del Instituto de Salud Carlos III, and F.D. is supported by grants from RTICCS from Instituto de Salud Carlos III and FEDER.

Financial disclosures: None declared.

Acknowledgments: We thank Dr. F. Barros, Dr. M. De la Fuente, Dr. A. Fernández-Marmiesse, and M. Pastoriza for technical support and Peter Rees for the English language correction.


   Footnotes
 
1 Nonstandard abbreviations: 21OHD, 21-hydroxylase deficiency; 21OH, steroid 21-hydroxylase; qPCR, quantitative PCR; Ct, threshold cycle; {Delta}Ct, difference in Cts between CYP21A2 and DSP genes.

2 Human genes: CYP21A2, gene encoding steroid 21-hydroxylase enzyme (cytochrome P450, family 21, subfamily A, polypeptide 2). Older nomenclature CYP21, CYP21B; CYP21A1P pseudogene (cytochrome P450, family 21, subfamily A, polypeptide 1 pseudogene). Older nomenclature CYP21P, CYP21A; DSP, gene that encodes desmoplakin protein.


   References
Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

  1. Speiser PW, White PC. Congenital adrenal hyperplasia. N Engl J Med 2003;349:776-788.[Free Full Text]
  2. Werkmeister JW, New MI, Dupont B, White PC. Frequent deletion and duplication of the steroid 21-hydroxylase genes. Am J Hum Genet 1986;39:461-469.[Web of Science][Medline] [Order article via Infotrieve]
  3. Collier S, Sinnott PJ, Dyer PA, Price DA, Harris R, Strachan T. Pulsed field gel electrophoresis identifies a high degree of variability in the number of tandem 21-hydroxylase and complement C4 gene repeats in 21-hydroxylase deficiency haplotypes. EMBO J 1989;8:1393-1402.[Web of Science][Medline] [Order article via Infotrieve]
  4. Haglund-Stengler B, Ritzen ME, Gustafsson J, Luthman H. Haplotypes of the steroid 21-hydroxylase gene region encoding mild steroid 21-hydroxylase deficiency. Proc Natl Acad Sci U S A 1991;88:8352-8356.[Abstract/Free Full Text]
  5. Sinnott PJ, Costigan C, Dyer PA, Harris R, Strachan T. Extended MHC haplotypes and CYP21/C4 gene organisation in Irish 21-hydroxylase deficiency families. Hum Genet 1991;87:361-366.[Web of Science][Medline] [Order article via Infotrieve]
  6. Sinnott PJ, Livieri C, Sampietro M, Marconi M, Harris R, Severi F, Strachan T. CYP21/C4 gene organisation in Italian 21-hydroxylase deficiency families. Hum Genet 1992;88:545-551.[Web of Science][Medline] [Order article via Infotrieve]
  7. Gitelman SE, Bristow J, Miller WL. Mechanism and consequences of the duplication of the human C4/P450c21/gene X locus. [Erratum in Mol Cell Biol 1992;12:3313–4]Mol Cell Biol 1992;12:2124-2134.[Abstract/Free Full Text]
  8. Wedell A, Stengler B, Luthman H. Characterization of mutations on the rare duplicated C4/CYP21 haplotype in steroid 21-hydroxylase deficiency. Hum Genet 1994;94:50-54.[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
  9. Yang Z, Mendoza AR, Welch TR, Zipf WB, Yu CY. Modular variations of the human major histocompatibility complex class III genes for serine/threonine kinase RP, complement component C4, steroid 21-hydroxylase CYP21, and tenascin TNX (the RCCX module). A mechanism for gene deletions and disease associations. J Biol Chem 1999;274:12147-12156.[Abstract/Free Full Text]
  10. Blanchong CA, Zhou B, Rupert KL, Chung EK, Jones KN, Sotos JF, et al. Deficiencies of human complement component C4A and C4B and heterozygosity in length variants of RP-C4-CYP21-TNX (RCCX) modules in Caucasians: the load of RCCX genetic diversity on major histocompatibility complex-associated disease. J Exp Med 2000;191:2183-2196.[Abstract/Free Full Text]
  11. Koppens PFJ, Hoogenboezem T, Degenhart HJ. Carriership of a defective tenascin-X gene in steroid 21-hydroxylase deficiency patients: TNXB-TNXA hybrids in apparent large-scale gene conversions. Hum Mol Genet 2002;11:2581-2590.[Abstract/Free Full Text]
  12. Koppens PFJ, Hoogenboezem T, Degenhart HJ. Duplication of the CYP21A2 gene complicates mutation analysis of steroid 21-hydroxylase deficiency: characteristics of three unusual haplotypes. Hum Genet 2002;111:405-410.[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
  13. Koppens PFJ, Smeets HJM, Wijs IJ, Degenhart HJ. Mapping of a de novo unequal crossover causing a deletion of the steroid 21-hydroxylase (CYP21A2) gene and a non-functional hybrid tenascin-X (TNXB) gene. J Med Genet 2003;40:e53.[Free Full Text]
  14. Tusié-Luna MT, White PC. Gene conversions and unequal crossovers between CYP21 (steroid 21-hydroxylase gene) and CYP21P involve different mechanisms. Proc Natl Acad Sci U S A 1995;92:10796-10800.[Abstract/Free Full Text]
  15. White PC, Speiser PW. Congenital adrenal hyperplasia due to 21-hydroxylase deficiency. Endocr Rev 2000;21:245-291.[Abstract/Free Full Text]
  16. Donohoue PA, Jospe N, Migeon CJ, Van Dop C. Two distinct areas of unequal crossing over within the steroid 21-hydroxylase genes produce absence of CYP21B. [Erratum in Genomics 1990;6:392]Genomics 1989;5:397-406.[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
  17. White PC, Vitek A, Dupont B, New MI. Characterization of frequent deletions causing steroid 21-hydroxylase deficiency. Proc Natl Acad Sci U S A 1988;85:4436-4440.[Abstract/Free Full Text]
  18. Lobato MN, Aledo R, Meseguer A. High variability of CYP21 gene rearrangements in Spanish patients with classic form of congenital adrenal hyperplasia. Hum Hered 1998;48:216-225.[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
  19. Lee HH, Chang SF, Lee YJ, Raskin S, Lin SJ, Chao MC, et al. Deletion of the C4-CYP21 repeat module leading to the formation of a chimeric CYP21P/CYP21 gene in a 9.3-kb fragment as a cause of steroid 21-hydroxylase deficiency. Clin Chem 2003;49:319-322.[Free Full Text]
  20. Koppens PFJ, Degenhart HJ. PCR-based detection of CYP21 deletions. Clin Chem 2003;49:1555-1556.[Free Full Text]
  21. Lee HH, Chan JG, Tsai CH, Tsai FJ, Chao HT, Chung B. Analysis of the chimeric CYP21P/CYP21 gene in steroid 21-hydroxylase deficiency. Clin Chem 2000;46:606-611.[Abstract/Free Full Text]
  22. Tukel T, Uyguner O, Wei JQ, Yksel-Apak M, Saka N, Song DX, et al. A novel semiquantitative polymerase chain reaction/enzyme digestion-based method for detection of large scale deletions/conversions of the CYP21 gene and mutation screening in Turkish families with 21-hydroxylase deficiency. J Clin Endocrinol Metab 2003;88:5893-5897.[Abstract/Free Full Text]
  23. Lee HH, Lee YJ, Lin CY. PCR-based detection of the CYP21 deletion and TNXA/TNXB hybrid in the RCCX module. Genomics 2004;83:944-950.[CrossRef][Web of Science][Medline] [Order article via Infotrieve]
  24. Lee HH, Lee YJ, Chan P, Lin CY. Use of PCR-based amplification analysis as a substitute for Southern blot method for CYP21 deletion detection in congenital adrenal hyperplasia. [Erratum in Clin Chem 2005;51:480]Clin Chem 2004;50:1074-1076.[Free Full Text]
  25. Olney RC, Mougey EB, Wang J, Shulman DI, Sylvester JE. Using real-time, quantitative PCR for rapid genotyping of the steroid 21-hydroxylase gene in a north Florida population. J Clin Endocrinol Metab 2002;87:735-741.[Abstract/Free Full Text]
  26. Loidi L, Quinteiro C, Parajes S, Barreiro J, Leston DG, Cabezas-Agricola JM, et al. High variability in CYP21A2 mutated alleles in Spanish 21-hydroxylase deficiency patients, six novel mutations and a founder effect. Clin Endocrinol 2006;64:330-336.[CrossRef][Medline] [Order article via Infotrieve]
  27. Rasmussen R. Quantification on the LightCycler. Meuer S Wittwer C Nakagawara K eds. Rapid Cycle Real-time PCR, Methods and Applications 2001:21-34 Springer Press Heidelberg. .
  28. L’Allemand D, Tardy V, Grüters A, Schnabel D, Krude H, Morel Y. How a patient homozygous for a 30-kb deletion of the C4-CYP21 genomic region can have a nonclassic form of 21-hydroxylase deficiency. J Clin Endocrinol Metab 2000;85:4562-4567.[Abstract/Free Full Text]



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S. Kleinle, R. Lang, G. F. Fischer, H. Vierhapper, F. Waldhauser, M. Fodinger, and S. M. Baumgartner-Parzer
Duplications of the Functional CYP21A2 Gene Are Primarily Restricted to Q318X Alleles: Evidence for a Founder Effect
J. Clin. Endocrinol. Metab., October 1, 2009; 94(10): 3954 - 3958.
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